Mercurial > repos > iuc > faffy_extract
changeset 1:30c0d75a8e9c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/faffy commit 9eb0e8172b3ac29d96aa9f28a89bc1d60fc11ec6
| author | iuc |
|---|---|
| date | Thu, 05 Mar 2026 14:17:08 +0000 |
| parents | 38362b891f98 |
| children | |
| files | faffy_extract.xml macros.xml test-data/paffy_add_mismatches_output.paf test-data/paffy_chain_output.paf test-data/paffy_dedupe_input.paf test-data/paffy_dedupe_input.paf.gz test-data/paffy_tile_output.paf test-data/simCow.chr6.range.fasta test-data/simCow.chr6.range.fasta.bz2 test-data/simCow.chr6.range.fasta.gz test-data/simDog.chr6.range.fasta test-data/testPaf.paf test-data/testPaf.paf.gz test-data/testPafChunked.paf test-data/testPafChunked.paf.gz |
| diffstat | 15 files changed, 1 insertions(+), 25311 deletions(-) [+] |
line wrap: on
line diff
--- a/faffy_extract.xml Wed Mar 04 13:13:05 2026 +0000 +++ b/faffy_extract.xml Thu Mar 05 14:17:08 2026 +0000 @@ -30,7 +30,7 @@ <param argument="--flank" type="integer" min="0" value="10" label="Flanking size" help="Number of additional base pairs to include at each end of each extracted sequence"/> <param argument="--minSize" type="integer" min="0" value="100" label="Minimum sequence length" help="The minimum length of a sequence (before adding the flanks) to extract"/> <param argument="--skipMissing" type="boolean" truevalue="--skipMissing" falsevalue="" checked="false" label="Skip missing sequences" help="Skip BED intervals that reference missing sequences instead of causing an error"/> - <expand macro="params_conditional_compression_fasta"/> + <expand macro="params_conditional_compression"/> </inputs> <outputs> <data name="out_file" format="fasta" label="${tool.name} on ${on_string}">
--- a/macros.xml Wed Mar 04 13:13:05 2026 +0000 +++ b/macros.xml Thu Mar 05 14:17:08 2026 +0000 @@ -7,22 +7,6 @@ <token name="@TOOL_VERSION@">2.9.9</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">25.1</token> - <token name="@UNCOMPRESS_PAF@"><![CDATA[ - #if $input_paf.is_of_type('paf.gz') - gunzip -c '$input_paf' | - #else - cat '$input_paf' | - #end if - ]]> - </token> - <token name="@COMPRESS_PAF@"><![CDATA[ - #if $compression.type == 'gz' - | gzip -c > '$out_file' - #else - > '$out_file' - #end if - ]]> - </token> <token name="@UNCOMPRESS_FASTA@"><